Using Nanopore data

[indralesmanaa]

Hi! Is there any drawback if using data generated from Oxford Nanopore sequencing?

[tao-bioinfo]

Hi @indralesmanaa . Thank you for your suggestions. As far as I know, Nanopore sequencing is typically used for full-length metabarcoding, such as bacterial 16S rRNA or fungal ITS. The length of the MiFish amplicon is approximately 170 bp, which is too short for Nanopore sequencing. Therefore, for MiFish amplicons, traditional short-read sequencing is recommended.

Regarding potential drawbacks, I think the main difference lies in the method of generating ASVs (amplicon sequence variations). Nanopore sequencing requires a different pipeline compared to the VSEARCH method we have implemented here. We have not yet tested any Nanopore sequencing data but will consider it in future updates.

[tao-bioinfo]

Hi @indralesmanaa , we are making a major update on this pipeline and it will support Nanopore data. We got very excellent results on Nanopore testing datasets. Follow us at https://x.com/MitoFishDB